H7 hemagglutinin lineage identification

This is the nucleotide sequence data and the R files for the k-means clustering of the H7 hemagglutinin segment of Influenza A. 

H7_HA_IRDB_2019_1_14.fasta is the initial data downloaded from the Influenza Research Database

H7_HA_IRDB_2019_1_14_aligned_muscle.fasta is the sequence data aligned with Muscle

H7_HA_IRDB_2019_1_14_aligned_muscle_cleaned.fas is the aligned sequence data after problem sequence have been removed.

RNA_distances_HA_kmeans_analysis.R is the R code for carrying out the k-means clustering and diagnostics.

kmeans_clustering.pdf is the R-markdown generated document describing the R-code for k-means clustering.

clustered_HA_kmeans_RNA.csv are the results of the clustering

usearch_clustering.csv is a summary of the USEARCH results.

Clade_Alpha.tree - alpha clade phylogenetic tree

Clade_Beta.tree - beta clade phylogenetic tree

Clade A-D trees are the phylogenetic trees for clades A to D.

H7_HA_IRDB_2019_1_14_aligned_muscle_cleaned_fasttree_coloured.tree is the overview tree of all the sequences.